Tag: ecology

Volunteer “community scientists” do a pretty darn good job generating usable data

When museum-goers did a community science activity in an exhibit at the Field Museum (USA), the data they produced were largely accurate.

**Left:** *Cuong Pham, Jimmy Crigler, and Joshua Torres working on a community science platform in an exhibit at the Field Museum (photo by Melanie Pivarski, Roosevelt University).*
**Right:** *The microscopic leaves of a liverwort, a primitive plant that helps scientists track climate change (photo by Lauren Johnson, Field Museum*).

Original publication by the Field Museum

Ask any scientist — for every “Eureka!” moment, there’s a lot of less-than-glamorous work behind the scenes. Making discoveries about everything from a new species of dinosaur to insights about climate change entails some slogging through seemingly endless data and measurements that can be mind-numbing in large doses.

Community science shares the burden with volunteers who help out, for even just a few minutes, on collecting data and putting it into a format that scientists can use. But the question remains how useful these data actually are for scientists.

A new study, authored by a combination of high school students, undergrads and grad students, and professional scientists showed that when museum-goers did a community science activity in an exhibit, the data they produced were largely accurate, supporting the argument that community science is a viable way to tackle big research projects.

“It was surprising how all age groups from young children, families, youth, and adults were able to generate high-quality taxonomic data sets, making observations and preparing measurements, and at the same time empowering community scientists through authentic contributions to science,”
says Matt von Konrat (Field Museum, USA), an author of the paper in the journal Research Ideas and Outcomes (RIO Journal) and the head of plant collections at Chicago’s Field Museum.

“This study demonstrates the wonderful scientific outcomes that occur when an entire community comes together,”
says Melanie Pivarski, an associate professor of mathematics at Roosevelt University (USA) and the study’s lead author.

“We were able to combine a small piece of the Field Museum’s vast collections, their scientific knowledge and exhibit creation expertise, the observational skills of biology interns at Northeastern Illinois University (USA), led by our collaborator Tom Campbell, and our Roosevelt University student’s data science expertise. The creation of this set of high-quality data was a true community effort!”

The study focuses on an activity in an exhibition at the Field Museum, in which visitors could partake in a community science project. In the community science activity, museumgoers used a large digital touchscreen to measure the microscopic leaves photographs of plants called liverworts.

These tiny plants, the size of an eyelash, are sensitive to climate change, and they can act like a canary in a coal mine to let scientists know about how climate change is affecting a region. It’s helpful for scientists to know what kinds of liverworts are present in an area, but since the plants are so tiny, it’s hard to tell them apart. The sizes of their leaves (or rather, lobes — these are some of the most ancient land plants on Earth, and they evolved before true leaves had formed) can hint at their species. But it would take ages for any one scientist to measure all the leaves of the specimens in the Field’s collection. Enter the community scientists.

“Drawing a fine line to measure the lobe of a liverwort for a few hours can be mentally strenuous, so it’s great to have community scientists take a few minutes out of their day using fresh eyes to help measure a plant leaf. A few community scientists who’ve helped with classifying acknowledged how exciting it is knowing they are playing a helping hand in scientific discovery,”
says Heaven Wade, a research assistant at the Field Museum who began working on the MicroPlants project as an undergraduate intern.

Community scientists using the digital platform measured thousands of microscopic liverwort leaves over the course of two years.

“At the beginning, we needed to find a way to sort the high quality measurements out from the rest. We didn’t know if there would be kids drawing pictures on the touchscreen instead of measuring leaves or if they’d be able to follow the tutorial as well as the adults did. We also needed to be able to automate a method to determine the accuracy of these higher quality measurements,”
says Pivarski.

To answer these questions, Pivarski worked with her students at Roosevelt University to analyze the data. They compared measurements taken by the community scientists with measurements done by experts on a couple “test” lobes; based on that proof of concept, they went on to analyze the thousands of other leaf measurements. The results were surprising.

“We were amazed at how wonderfully children did at this task; it was counter to our initial expectations. The majority of measurements were high quality. This allowed my students to create an automated process that produced an accurate set of MicroPlant measurements from the larger dataset,”
says Pivarski.

The researchers say that the study supports the argument that community science is valuable not just as a teaching tool to get people interested in science, but as a valid means of data collection.

“Biological collections are uniquely poised to inform the stewardship of life on Earth in a time of cataclysmic biodiversity loss, yet efforts to fully leverage collections are impeded by a lack of trained taxonomists. Crowd-sourced data collection projects like these have the potential to greatly accelerate biodiversity discovery and documentation from digital images of scientific specimens,”
says von Konrat.

Research article:

Pivarski M, von Konrat M, Campbell T, Qazi-Lampert AT, Trouille L, Wade H, Davis A, Aburahmeh S, Aguilar J, Alb C, Alferes K, Barker E, Bitikofer K, Boulware KJ, Bruton C, Cao S, Corona Jr. A, Christian C, Demiri K, Evans D, Evans NM, Flavin C, Gillis J, Gogol V, Heublein E, Huang E, Hutchinson J, Jackson C, Jackson OR, Johnson L, Kirihara M, Kivarkis H, Kowalczyk A, Labontu A, Levi B, Lyu I, Martin-Eberhardt S, Mata G, Martinec JL, McDonald B, Mira M, Nguyen M, Nguyen P, Nolimal S, Reese V, Ritchie W, Rodriguez J, Rodriguez Y, Shuler J, Silvestre J, Simpson G, Somarriba G, Ssozi R, Suwa T, Syring C, Thirthamattur N, Thompson K, Vaughn C, Viramontes MR, Wong CS, Wszolek L (2022) People-Powered Research and Experiential Learning: Unravelling Hidden Biodiversity. Research Ideas and Outcomes 8: e83853. https://doi.org/10.3897/rio.8.e83853

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Endemic frogs in Himalayan region exhibit site fidelity

The Murree Hills Frog and Hazara Torrent Frog show minimum movement out of their habitat, which makes them more unique from an ecology and conservation perspective

Amongst tetrapods, amphibians entail the highest number of threatened and data deficient species, which has put them in the limelight of research in animal ecology and conservation. Endemic species have evolved and adapted to a particular set of environmental conditions. Hence, these are more vulnerable to environmental changes and are susceptible to population declines because of their restricted distribution ranges.

Murree Hills Frog (Nanorana vicina). Photo by Herpetology Lab, Arid Agriculture University, Rawalpindi

The Murree Hills Frog and Hazara Torrent Frog are endemic to Pakistan and South Asian countries. They are associated with the torrential streams and nearby clear water pools situated at high elevation. These frogs are susceptible to threats like habitat degradation, urbanization, and climate change. A recent study published in the-open access journal Biodiversity Data Journal reports that these endemic frogs do not show much movement within and outside their habitat.

Hazara Torrent Frog (Allopaa hazarensis). Photo by Herpetology Lab, Arid Agriculture University, Rawalpindi

“We have, for the first time, used radio-transmitters (VHF) on frogs endemic to Himalayan region to understand their ecology,” explains Dr. Muhammad Rais, Assistant Professor at the Herpetology Lab in the Arid Agriculture University, Rawalpindi, and lead author of the study. “Surprisingly, the Murree Hills Frog and Hazara Torrent Frog depend heavily for their survival on particular stream(s).”

“We suggest carrying out additional long term studies by incorporating multiple adjacent stream systems to better understand dispersal and colonization in these frogs,” he says in conclusion.

Research article:

Akram A, Rais M, Saeed M, Ahmed W, Gill S, Haider J (2022) Movement Paradigm for Hazara Torrent Frog Allopaa hazarensis and Murree Hills Frog Nanorana vicina (Anura: Dicroglossidae). Biodiversity Data Journal 10: e84365. https://doi.org/10.3897/BDJ.10.e84365

The first cave-bound mollusc species from the Americas

Against the odds, a study by Brazilian researchers describes a new to science species of evidently cave-bound – or troglobitic – clam from northern Brazil.

Exclusively subterranean bivalves – the group of molluscs comprising clams, oysters, mussels, scallops – are considered a rarity. Prior to the present study, there had only been three such species confirmed in the world: all belonging to a small-sized mussel genus known from southeastern Europe. Furthermore, bivalves are not your typical ‘underworld’ dweller, since they are almost immobile and do not tolerate environments low in oxygen.

Against the odds, a recent study by Dr. Luiz Ricardo L. Simone (Museum of Zoology of the University of São Paulo) and Dr Rodrigo Lopes Ferreira (Federal University of Lavras), published in the open-access scholarly journal Subterranean Biology, describes a new to science species of evidently cave-bound – or troglobitic – clam from northern Brazil.

Small individuals of the newly described clam species Eupera troglobia sp. n. exposed to the air, next to a harvestman (Eusarcus sp.). Photo by Rodrigo Lopes Ferreira.

Named Eupera troglobia, the mollusk demonstrates features characteristic for organisms not meant to see the daylight, including lack of pigmentation, reduced size, delicate shell and fewer, yet larger eggs.

Curiously, it was back in 2006 when a report presenting a faunal survey of a cave in northern Brazil featured photographs of what was to be described as Eupera troglobia. However, the evidence was quickly dismissed: the clam must have been carried into the cave by water.

A submerged specimen of the newly described cave-bound clam species Eupera troglobia sp. n.

In 2010, Dr Rodrigo Lopes Ferreira accessed the report and noticed the depigmentation of the clams. Wondering whether it was indeed possible that he was looking at a troglobite, he searched amongst the collected specimens from that study, but could not find any of the discoloured bivalve.

Ten years later, his team visited the cave to specifically search for depigmented shells. Although the cave was partially flooded, the researchers were able to spot the specimens they needed attached to the walls of the cave.

In conclusion, the scientists highlight that their discovery is the latest reminder about how important the conservation of the fragile subterranean habitats is, given the treasure troves in their holdings.

Meanwhile, recently amended laws in Brazil put caves at considerably higher risk.

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Research paper:

Simone LRL, Ferreira RL (2022) Eupera troglobia sp. nov.: the first troglobitic bivalve from the Americas (Mollusca, Bivalvia, Sphaeriidae). Subterranean Biology 42: 165-184. https://doi.org/10.3897/subtbiol.42.78074

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Novel research seeks to solve environmental challenges in BioRisk’s latest issue

The special issue features 35 studies presented at the International Seminar of Ecology 2021

Guest blog post by Prof. Stephka Chankova, PhD

The new special issue of BioRisk compiles materials presented at the International Seminar of Ecology – 2021. The multidisciplinary nature of modern ecology was demonstrated by the main topics of the Seminar: biodiversity and conservation biology, biotic and abiotic impact on the living nature, ecological risk and bioremediation, ecosystem research and services, landscape ecology, and ecological agriculture.

Research teams from various universities, institutes, organizations, and departments, both from Bulgaria and abroad, took part in the Seminar. Foreign participants included: Environmental Toxicology Research Unit (Egypt), Pesticide Chemistry Department, National Research Centre (Giza, Egypt); National Institute for Agrarian and Veterinary Research (Oeiras, Portugal), Centre for Ecology, Evolution and Environmental Changes (Lisbon, Portugal); Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences (Moscow, Russia).

Biorisk’s latest issue: Current trends of ecology

Some of the reports presented joint research of Bulgarian scientists and scientists from Germany, the Czech Republic, Lithuania, Romania, Slovenia, Spain, and the USA. After assessment by independent reviewers, the articles published in the journal cover the topics presented and discussed at the Seminar.

A set of reports were focused on the anthropogenic and environmental impacts on the biota. Soil properties were shown as a factor that can modulate the effect of heavy metals, present in chronically contaminated soils. Different approaches to overcome environmental pollution were presented and discussed: zeolites as detoxifying tools, microalgae for the treatment of contaminated water bodies, and a newly developed bio-fertilizer, based on activated sludge combined with a bacterial strain with detoxifying and plant growth-promoting properties. The clear need for the enlargement of existing monitoring program by including more bioindicators and markers was pointed out.

It was shown that, by using various markers for the evaluation of environmentally induced stress response at different levels (microbiological, molecular, biochemical), it is possible to gain insights of the organisms’ protection and the mechanisms involved in resistance formation. The contribution of increased DNA repair capacity and AOS to the development of environmental tolerance or adaptation was also shown.

Important results for understanding the processes of photoprotection in either cyanobacteria or algae, and higher plants were obtained by in vitro reconstitution of complexes of stress HliA protein with pigments. The crucial role of the cellular physiological state, as a critical factor in determining the resistance to environmental stress with Q cells was demonstrated.

Several papers were focused on the action of bioactive substances of plants origin. The bioactivity was shown to depend strongly on chemical composition. Origanum vulgare hirtum essential oil was promoted as a promising candidate for the purposes of “green” technologies. Analyzing secondary metabolites of plants, it was shown that their productivity in vitro is a dynamic process closely related to the plant growth and development, and is in close relation with the interactions of the plant with the environment.

Origanum vulgare hirtum. Photo by cultivar413 under a CC-BY 2.0 license

The influence of the agricultural system type on essential oil production and antioxidant activity of industrially-cultivated Rosa damascena in the Rose valley (Bulgaria) was reported, comparing organic vs conventional farming. The rose extracts from organic farming were shown to accumulate more phenolic compounds, corresponding to the higher antioxidant potential of organic roses.

A comparative study, based on official data from the statistics office of the EU and the Member countries, concerning viral infection levels in intensive and organic poultry farming, demonstrated that free-range production had a higher incidence of viral diseases with a high zoonotical potential.

Pollinators of Lavandula angustifolia, as an important factor for optimal production of lavender essential oil, were analyzed. It was concluded that, although lavender growers tend to place beehives in the fields for optimal essential oil production, it was crucial to preserve wild pollinators, as well.

*Lavandula angustifolia* inflorescence excluded from pollinators.

New data reported that essential oils and alkaloid-rich plant extracts had the strongest acetylcholinesterase inhibitory activity and could be proposed for further testing for insect control.

It was reported that the vegetation diversity of Bulgaria had still not been fully investigated. Grasslands, broad-leaved forests, and wetlands are the best investigated habitats, while data concerning ruderal, shrubland, fringe, and chasmophytic vegetation in Bulgaria are scarce.

Other important topics were reported and discussed in this session: the possibility of pest control using pteromalids as natural enemies of pests in various crops; the main reasons responsible for the population decrease of bumblebees – habitat destruction, loss of floral resources, emerging diseases, and increased use of pesticides (particularly neonicotinoids); the strong impact of temperature and wind on the distribution of zooplankton complexes in Mandra Reservoir, in Southeastern Bulgaria; an alternative approach for the ex-situ conservation of Stachys thracica based on in vitro shoot culture and its subsequent adaptation under ex vitro conditions.

*Bombus hortorum/subterraneus collecting* nectar in 1991, and B *B. wurflenii/lapidarius* worker robbing nectar of *Gentiana asclepiadea* in 2017

New information was presented concerning pre-monitoring geochemical research of river sediments in the area of Ada Tepe gold mining site (Eastern Rhodopes). The obtained results illustrate that the explored landscapes have been influenced by natural geochemical anomalies, as well as, impacted by human activity. The forests habitat diversity of Breznik Municipality was revealed, following the EUNIS Classification and initial data from the Ministry of Environment and Water and the Forestry Management Plans. It was shown that, in addition to the dominant species Quercus dalechampii, Quercus frainetto, Fagus sylvatica, Carpinus betulus, some artificial plantations with Pinus nigra and Pinus sylvestris were also present, as well as non-native species, such as Robinia pseudoacacia and Quercus rubra.

Models for Predicting Solution Properties and Solid-Liquid Equilibrium in Cesium Binary and Mixed Systems were created. The results are of great importance for the development of strategies and programs for nuclear waste geochemical storage. In conclusion, many results in different areas of ecology were presented in the Seminar, followed by interesting discussions. A lot of questions were answered, however many others remained open. A good platform for further discussion will be the next International Seminar of Ecology – 2022, entitled Actual Problems of Ecology.

Major highway in India threatens reptiles and amphibians

“Is it the road that crosses the habitat, or does the habitat cross the road?” ask scientists before agreeing that the wrong road at the wrong place is bound to cause various perils for the local wildlife, habitats and ecosystems.

“Is it the road that crosses the habitat, or does the habitat cross the road?” ask scientists at Gauhati University (Assam, India) before agreeing that the wrong road at the wrong place is bound to cause various perils for the local wildlife, habitats and ecosystems. Furthermore, some of those effects may take longer than others to identify and confirm.

This is how the research team of doctoral research fellow Somoyita Sur, Dr Prasanta Kumar Saikia and Dr Malabika Kakati Saikia decided to study roadkill along a 64-kilometre-long stretch of one of the major highways in India: the National Highway 715.

What makes the location a particularly intriguing choice is that it is where the highway passess between the Kaziranga National Park, a UNESCO World Heritage site in Assam and the North Karbi Anglong Wildlife Sanctuary, thus tempting animals to move to and from the floodplains of Kaziranga and the hilly terrain of the Sanctuary to escape the annual floods or – on a daily basis – in search for food and mating partners.

In the beginning, they looked into various groups, including mammals, birds, reptiles, and amphibians, before realising that the death toll amongst frogs, toads, snakes and lizards was indeed tremendous, yet overlooked. Their findings were recently published in the peer-reviewed scholarly journal Nature Conservation.

“To our surprise, the death toll within that 64-kilometre stretch of the highway was indeed dramatic. We estimated that it has been over 6000 animals that have fallen under the wheels of motor vehicles within a single year. Prior to our study, similar research had focused on big charismatic species like the tiger, elephant and rhino, so when we took into account also the smaller animals: frogs, toads, snakes and lizards, the count went through the roof. Thus, we decided to make smaller species the focus of our work,”
comments Sur.

In conclusion, the scientists agree that roads and highways cannot be abandoned or prevented from construction and expansion, as they are crucial in connecting people and transporting goods and necessities.

“Yet, we can definitely put some effort into designing and constructing them in a scientifically sound, eco-friendly and sustainable manner, so that they don’t become the bane for our ecosystems,”
the team concludes.

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Research article:

Sur S, Saikia PK, Saikia MK (2022) Speed thrills but kills: A case study on seasonal variation in roadkill mortality on National highway 715 (new) in Kaziranga-Karbi Anglong Landscape, Assam, India. In: Santos S, Grilo C, Shilling F, Bhardwaj M, Papp CR (Eds) Linear Infrastructure Networks with Ecological Solutions. Nature Conservation 47: 87-104. https://doi.org/10.3897/natureconservation.47.73036

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Invasive crayfish can cause high fisheries damage

In Zambia and Zimbabwe, a single crayfish may cause annual fishery losses of as much as $6.15

Guest blog post by Josie South

Invasive crayfish have the potential to cause high economic cost to artisanal fisheries in southern Africa through scavenging behaviour and destroying fish fry habitat.

A recent study by C∙I∙B Research Associate Josie South (University of Leeds, UK) with scientists from the South African Institute for Aquatic Biodiversity (SAIAB) quantified the damage caused by two invasive crayfish compared to native crab species, at two temperatures, on tilapia catch and macrophytes.

Redclaw crayfish entangled in a gill net in the Kafue River. Photo by Bruce Ellender

Economic costs of invasive species are vital to prioritise and incentivise management spending to reduce and restrict invasive species. No economic costs have been published for the global invader – the redclaw crayfish (Cherax quadricarinatus), and none for the entire continent of Africa. Another prolifically invasive crayfish, the red swamp crayfish (Procambarus clarkii) is also invasive in various countries of southern Africa. Anecdotal reports of crayfish scavenging from artisanal gillnet fisheries are abundant across the invasive ranges but lacked quantification. Similarly anecdotal information about macrophyte stands being destroyed by crayfish has been reported.

For their study, Josie and colleagues compared the feeding rates per gram of crayfish to that of the native Potamonautid crabs at 19°C and 28°C on simulated fisheries catch and macrophytes to identify how much damage may be caused.

Gill net fish catch damaged by crayfish scavenging. Photo by Josie South

The red swamp crayfish consumed the most macrophytes regardless of temperature, at a higher rate than the redclaw crayfish or crabs. In contrast, redclaw crayfish consumed the most tilapia regardless of temperature, and targeted the tail, abdomen, and fins whereas the crab only consumed the head of the fish. The damage rates of redclaw crayfish were then combined with average mass of crayfish in three invasion cores in Zambia and Zimbabwe. It was found that the damage one crayfish may cause annual fishery losses from $6.15 (Kafue River); $5.42 (Lake Kariba); and $3.62 (Barotse floodplain).

Inland fisheries contribute substantially to the livelihoods and quality of life in Africa. The two invasive crayfish have different capacities for ecological and socio-economic impact depending on the resource and the temperature which means that impact assessments should not be generalised across species.

Redclaw crayfish capacity to damage fish catch was substantial but this should be caveated with two over/under estimation issues: 1) the potential for fisher behavioural change which may reduce crayfish damage and 2) small damage to the fish may render the catch unsaleable and therefore the cost of the whole fish is lost.

Dr Josie South states that while these data are a crucial first step in filling knowledge gaps in crayfish impacts in Africa, it also stresses the need to derive observed costs from fisheries dependent data to avoid misleading estimates.

Also of concern, is the capacity for ecological and socio-economic damage from the red swamp crayfish, which was recently removed from the NEM:BA regulations of prohibited species due to lack of impact evidence.

Read the paper published in NeoBiota

Madzivanzira TC, Weyl OLF, South J (2022) Ecological and potential socioeconomic impacts of two globally-invasive crayfish. NeoBiota 72: 25–43. https://doi.org/10.3897/neobiota.72.71868

This blog post was first published by DSI-NRF Centre for Invasion Biology, Stellenbosch University.

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Citizen science data crucial to understand wildlife roadkill

In a first for science, researchers set out to analyze over 10 years of roadkill records in Flanders, Belgium, using data provided by citizen scientists.

The road is a dangerous place for animals: they can easily get run over, which can seriously affect wildlife diversity and populations in the long term. There is also a human economic cost and possible injury or even death in these accidents, while crashing into heavier animals or trying to avoid them on the road.

Making roads safer for both animals and people starts with a simple first step: understanding when, where, and how many animals get run over. This knowledge can help protect specific species, for example by using warning signs, preventing access to the roads for animals, creating overpasses and underpasses, or closing roads. Wildlife roadkill data can also help monitor other trends, such as population dynamics, species distribution, and animal behavior.

Thanks to citizen science platforms, obtaining this kind of data is no longer a task reserved for scientists. There are now dozens of free, easy-to-use online systems, where anyone can record wildlife collision accidents or roadkill, contributing to a fuller picture that might later be used to inform policy measures.

One such project is the Flemish Animals under wheels, where users can register the roadkill they saw, adding date, time and geolocation online or by using the apps. The data is stored in the online biodiversity database Waarnemingen.be, the Flemish version of the international platform Observation.org.

Between 2008 and 2020, the project collected almost 90,000 roadkill records from Flanders, Belgium, registered by over 4,000 citizen scientists. Roadkill recording is just a small part of their nature recording activities – the multi-purpose platform which also allows the registration of living organisms. This is probably why the volunteers have remained engaged with the project for over 6 years now.

In a first for science, researchers from Natuurpunt Studie, the scientific institute linked to the largest Nature NGO in Flanders, with support from the Department of Environmental and Spatial Development, set out to analyze over 10 years of roadkill records in the region, using data provided by citizen scientists. In their study, published in the peer-reviewed journal Nature Conservation, they focused on 17 key species of mammals and their fate on the roads of Flanders.

The researchers analyzed data on 145,000 km of transects monitored, which resulted in records of 1,726 mammal and 2,041 bird victims. However, the majority of the data – over 60,000 bird and mammal roadkill records – were collected opportunistically, where opportunistic data sampling favors larger or more “enigmatic” species. Hedgehogs, red foxes and red squirrels were the most frequently registered mammal roadkill victims.

In the last decade, roadkill incidents in Flanders have diminished, the study found, even though search effort increased. This might be the result of effective road collision mitigation, such as fencing, crossing structures, or animal detection systems. On the other hand, it could be a sign of declining populations among those animals that are most prone to being killed by vehicles. More research is needed to understand the exact reason. Over the last 11 years, roadkill records of the European polecat showed a significant relative decrease, while seven species, including the roe deer and wild boar, show a relative increase in recorded incidents.

There seems to be a clear influence of the COVID-19 pandemic on roadkill patterns for some species. Restrictions in movement that followed likely led simultaneously to fewer casualties and a decrease in the search effort.

The number of new observations submitted to Waarnemingen.be continues to increase year after year, with data for 2021 pointing to about 9 million. Even so, the scientists warn that those recorded observations “are only the tip of the iceberg.”

“Citizen scientists are a very valuable asset in investigating wildlife roadkill. Without your contributions, roadkill in Flanders would be a black box,”
the researchers conclude.

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Research paper:

Swinnen KRR, Jacobs A, Claus K, Ruyts S, Vercayie D, Lambrechts J, Herremans M (2022) ‘Animals under wheels’: Wildlife roadkill data collection by citizen scientists as a part of their nature recording activities. In: Santos S, Grilo C, Shilling F, Bhardwaj M, Papp CR (Eds) Linear Infrastructure Networks with Ecological Solutions. Nature Conservation 47: 121-153. https://doi.org/10.3897/natureconservation.47.72970

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The research article is part of the Special Issue: “Linear Infrastructure Networks with Ecological Solutions“, which collates 15 research papers reporting on studies presented at the IENE2020 conference.

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Simplified method to survey amphibians will aid conservation

Researchers developed a method to determine which amphibians inhabit a specific area. The new technique will resolve some of the issues with conventional methods, such as capture and observational surveys.

Ryukyu Sword Tailed Newt, or Firebellied Newt. *Photo by Neil Dalphin via Creative Commons CC0.*

An international collaborative research group of members from seven institutions has developed a method to determine which amphibians (frogs, newts and salamanders) inhabit a specific area. Their work was published in the open-access, peer-reviewed journal Metabarcoding and Metagenomics (MBMG).

To do so, the scientists amplified and analysed extra-organismal DNA (also known as environmental DNA or eDNA) found in the water. This DNA ends up in the water after being expelled from the amphibian’s body along with mucus and excrement.

The research group included Postdoctoral Researcher Sakata K. Masayuki and Professor Minamoto Toshifumi (Kobe University), Associate Professor Kurabayashi Atsushi (Nagahama Institute of Bio-Science and Technology), Nakamura Masatoshi (IDEA Consultants, Inc.) and Associate Professor Nishikawa Kanto (Kyoto University).

The newly developed technique will resolve some of the issues with conventional methods, such as capture and observational surveys, which require a specialist surveyor who can visually identify species. Conventional surveys are also prone to discrepancies due to environmental factors, such as climate and season.

The researchers hope that the new method will revolutionise species monitoring, as it will enable anyone to easily monitor the amphibians that inhabit an area by collecting water samples.

While monitoring in general is crucial to conserve the natural ecosystems, the importance of surveying amphibians is even more pressing, given the pace of their populations’ decline.

Amongst major obstacles to amphibian monitoring, however, are the facts that they are nocturnal; their young (e.g. tadpoles) and adults live in different habitats; and that specialist knowledge is required to capture individuals and identify their species. These issues make it particularly difficult to accurately survey amphibians in a standardised way, and results of individual efforts often contradict each other.

On the other hand, eDNA analysis techniques have already been established in programmes targeted at monitoring fish species, where they are already commonplace. So, the researchers behind the present study joined forces to contribute towards the development of a similar standardised analysis method for amphibians.

First of all, the researchers designed multiple methods for analysing the eDNA of amphibians and evaluated their performance to identify the most effective method. Next, they conducted parallel monitoring of 122 sites in 10 farmlands across Japan using the developed eDNA analysis along with the conventional methods (i.e. capture surveys using a net and observation surveys).

As a result, the newly developed method was able to detect all three orders of amphibians: Caudata (the newts and salamanders), Anura (the frogs), and Gymnophiona (the caecilians).

Furthermore, this novel eDNA analysis method was able to detect more species across all field study sites than the conventional method-based surveys, indicating its effectiveness.

Research Background

Amphibian biodiversity is continuing to decline worldwide and collecting basic information about their habitats and other aspects via monitoring is vital for conservation efforts. Traditional methods of monitoring amphibians include visual and auditory observations, and capture surveys.

However, amphibians tend to be small in size and many are nocturnal. The success of surveys varies greatly depending on the climate and season, and specialist knowledge is required to identify species. Consequently, it is difficult to monitor a wide area and assess habitats. The last decade has seen the significant development of environmental DNA analysis techniques, which can be used to investigate the distribution of a species by analysing external DNA (environmental DNA) that is released into the environment along with an organism’s excrement, mucus and other bodily fluids.

The fundamentals of this technique involve collecting water from the survey site and analysing the eDNA contained in it to find out which species inhabit the area. In recent years, the technique has gained attention as a supplement for conventional monitoring methods. Standardised methods of analysis have already been established for other species, especially fishes, and diversity monitoring using eDNA is becoming commonplace.

However, eDNA monitoring of amphibians is still at the development stage. One reason for this is that the proposed eDNA analysis method must be suitable for the target species or taxonomic group, and there are still issues with developing and implementing a comprehensive method for detecting amphibians. If such a method could be developed, this would make it possible for monitoring to be conducted even by people who do not have the specialised knowledge to identify species nor surveying experience.

Hopefully, this would be established as a unified standard for large-scale monitoring surveys, such as those on a national scale. This research group’s efforts to develop and evaluate analysis methods will hopefully lay the foundations for eDNA analysis to become a common tool for monitoring amphibians, as well as fish.

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Research article:

Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T (2022) Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. Metabarcoding and Metagenomics 6: e76534. https://doi.org/10.3897/mbmg.6.76534

Extensive practical guide to DNA-based biodiversity assessment methods published as a ‘living’ document by DNAqua-Net COST Action

Between 2016 and 2021, over 500 researchers collaborated within the DNAqua-Net international network, funded by the European Union’s European Cooperation in Science and Technology programme (COST), with the goal to develop and advance biodiversity assessment methods based on analysis of DNA obtained from the environment (e.g. river water) or from unsorted collections of organisms.

Such innovative methods are a real game changer when it comes to large-scale assessment of biodiversity and ecological monitoring, as collecting environmental samples that are sent to the lab for analysis is much cheaper, faster and non-invasive, compared with capturing and examining live organisms. However, large-scale adoption has been hindered by a lack of standardisation and official guidance.

Recognising the urgent need to scale up ecological monitoring as we respond to the biodiversity and climate crises, the DNAqua-Net team published a guidance document for the implementation of DNA-based biomonitoring tools.

The guide considers four different types of samples: water, sediments, invertebrate collections and diatoms, and two primary analysis types: single species detection via qPCR and similar targeted methods; and assessment of biological communities via DNA metabarcoding. At each stage of the field and laboratory process the guide sets out the scientific consensus, as well as the choices that need to be made and the trade-offs they entail. In particular, the guide considers how the choices may be influenced by common practical constraints such as logistics, time and budget. Available in an Advanced Book format, the guidelines will be updated as the technology continues to evolve.

Leaders of DNAqua-Net are Prof. Dr. Florian Leese of the University of Duisburg-Essen (Germany) and Dr. Agnès Bouchez of the French National Institute for Agriculture, Food, and Environment (INRAE). The core writing team for the present guide book involves Dr. Micaela Hellström (MIX Research AB, Sweden), Dr. Kat Bruce (NatureMetrics Ltd., UK), Dr. Rosetta Blackman (University of Zurich and EAWAG, Switzerland), Dr. Sarah Bourlat (LIB/Museum Koenig, Germany), and Prof. Kristy Deiner (ETH Zurich and SimplexDNA AG, Switzerland).

“Back in 2016 we realised that all around the globe researchers are testing new eDNA methods, developing individual solutions and products. While this is excellent, we need to reach a consensus and provide this consensus to stakeholders from the applied sectors”,
says Florian Leese.

This video was created as part of EU COST Action DNAqua-Net (CA15219) and shows how environmental DNA (eDNA) can be sampled and analysed from aquatic ecosystems. It shows the whole cycle from the start to final results.
Credit: DNAqua-Net

The guide’s lead author Dr. Kat Bruce adds:

“The urgency of addressing the twin biodiversity and climate crises means that we need to accelerate the adoption of new technologies that can provide data and insights at large scales. In doing so, we walk a tricky line to agree on sufficiently standardised methods that can be usefully applied as soon as they add value, while still continuing to develop them further and innovate within the field. It was a daunting task to seek consensus from several hundred scientists working in a fast-moving field, but we found that our technology is based on a strong foundation of knowledge and there was a high level of agreement on the core principles – even if the details vary and different users make different choices depending on their environmental, financial or logistical constraints.”

Looking back on the last four years that culminated in the publication of a “living” research publication, Prof. Dr. Kristy Deiner says:

“The document took many twists and turns through more than ten versions and passionate discussions across many workshops and late night drinks. All in the days when we could linger at conferences without fear of the pandemic weighing on us. As we worked to find consensus, one thing was clear: we had a lot to say and a standard review paper was not going to cut it. With the knowledge and experience gathered across the DNAqua-Net, it made sense to not limit this flow of information, but rather to try and tackle it head on and use it to address the many questions we’ve all struggled with while developing DNA-based biodiversity survey methods.”

Now that the document – or at least its first version – is publicly available, the researchers are already planning for the next steps and challenges.

“The bottom line is we’ve come a long way in the last ten years. We have a buffet of methods for which many produce accurate, reliable and actionable data to the aid of biodiversity monitoring and conservation. While there is still much work to be done, the many unanswered questions are because the uptake is so broad. With this broad uptake comes novel challenges, but also new insights and a diversity of minds with new ideas to address them. As said this is planned to be a living document and we welcome continued inputs no matter how great or small,” says Deiner.

Dr. Micaela Hellström recalls:

“The book evolved over the four years of COST Action DNAqua-Net which made it possible for the many scientists and stakeholders involved to collaborate and exchange knowledge on an unprecedented scale. Our whole team is well aware of the urgent need to monitor biodiversity loss and to provide accurate species distribution information on large scales, to protect the species that are left. This was a strong driving force for all of us involved in the production of this document. We need consensus on how to coherently collect biodiversity data to fully understand changes in nature.”

“It was a great and intense experience to be a part of the five-person core writing team. In the months prior to submitting the document, we spent countless hours, weekends and late nights researching the field, communicating with researchers and stakeholders, and joining vivid Zoom discussions. As a result, the present book provides solid guidance on multiple eDNA monitoring methods that are – or will soon become – available as the field moves forward.”

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The DNAqua-Net team invites fellow researchers and practitioners to provide their feedback and personal contributions using the contacts below.

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Original source:

Bruce K, Blackman R, Bourlat SJ, Hellström AM, Bakker J, Bista I, Bohmann K, Bouchez A, Brys R, Clark K, Elbrecht V, Fazi S, Fonseca V, Hänfling B, Leese F, Mächler E, Mahon AR, Meissner K, Panksep K, Pawlowski J, Schmidt Yáñez P, Seymour M, Thalinger B, Valentini A, Woodcock P, Traugott M, Vasselon V, Deiner K (2021) A practical guide to DNA-based methods for biodiversity assessment. Advanced Books. https://doi.org/10.3897/ab.e68634

First moth species on Alpenrose discovered

Discovery of the first moth species to mine the leaves of the highly poisonous Alpine rose

Rust-red alpine rose, one of the most popular alpine plants. Photo by Ingrid Huemer

An Austrian-Swiss research team was able to find a previously unknown glacial relic in the Alps, the Alpine rose leaf-miner moth. It is the first known species to have its caterpillars specializing on the rust-red alpine rose, a very poisonous, widely distributed plant that most animals, including moths and butterflies, strictly avoid. The extraordinary record was just published in the peer-reviewed scientific journal Alpine Entomology.

Poisonous host plant

The rust-red alpine rose (Rhododendron ferrugineum) is among the best-known and most attractive plants due to its flowering splendor – at least for humans. It is, in fact, a highly poisonous plant, strictly avoided by grazing animals. For insects, the alpine rose is attractive at most as a nectar plant; insect larvae, on the other hand, develop on it only in exceptional cases. This also applies to Alpine butterflies and moths, which leave Alpine roses largely untouched despite their wide distribution. Therefore, the discovery of a highly specialized species in the Alps came as a complete surprise.

Chance find

Alpine rose leaf-miner moth adults resting on leaves of the host-plant in Ardez, Graubünden, Switzerland. Photos by Jürg Schmid

Since alpine roses are unattractive to caterpillars and no insect the entire Alpine region was previously known to specialize on them, butterfly and moth experts had considered them rather uninteresting and ignored them in their research. The discovery of the alpine rose leaf-miner wasn’t the result of a targeted search: it was a pure stroke of luck.

During a cloudy spell in July this year, researchers surveying the butterflies in Ardez in the Engadine valley, Switzerland, happened to take a break exactly at an infested alpine rose bush.

“The accidental sighting of the first caterpillar in an alpine rose leaf was an absolute adrenaline rush, it was immediately clear that this must be an extraordinary species,”
Peter Huemer, researcher and head of the natural sciences department of the Tyrolean State Museums

Peter Huemer, researcher and head of the natural sciences department of the Tyrolean State Museums, and Swiss butterfly and moth expert Jürg Schmid came back in late July and early August to look for caterpillars and pupae and find out more about this curious insect. The extended search yielded evidence of a stable population of a species that was initially a complete enigma.

Life in the leaf

Leaf-mines of the alpine rose leaf-miner moth on *Rhododendron ferrugineum* in Ardez, Graubünden, Switzerland. Photos by Peter Huemer

The alpine rose leaf-miner moth drills through the upper leaf skin and into the leaf interior immediately after the caterpillar hatches. The caterpillar then spends its entire life until pupation between the intact leaf skins, eating the leaf from the inside. Thanks to this behavior, the caterpillar is just as well protected from bad weather as from many predators such as birds, spiders, or some carnivore insects. The feeding trail, called a leaf mine, begins with a long corridor and ends in a large square-like mine section. The feces are deposited inside this mine. When the time comes for pupation, the caterpillar leaves the infested leaf and makes a typical web on the underside or a nearby leaf. With the help of several fine silk threads, it produces an elaborate “hammock”, in which the pupation finally takes place. In the laboratory, after about 10 days, the successful breeding to a moth succeeded, with a striking result.

Enigmatic glacial relic

Final instar larva of the alpine rose leaf-miner moth on *Rhododendron ferrugineum* in Ardez, Graubünden, Switzerland. Photo by Jürg Schmid

Huemer and Schmid were surprised to find out that the moths belonged to a species that was widespread in northern Europe, northern Asia and North America – the swamp porst leaf-miner butterfly Lyonetia ledi. By looking at its morphological features, such as wing color and pattern, and comparing its DNA barcodes to those of northern European specimens, they were able to confirm its identity.

Habitat of the alpine rose leaf-miner moth in Engadine/Switzerland with *Rhododendron ferrugineum*. Photo by Jürg Schmid

The Engadine population, however, is located more than 400 km away from the nearest other known populations, which are on the border of Austria and the Czech Republic. Furthermore, the species lives in northern Europe exclusively on swamp porst and Gagel bush – two shrubs that are typical for raised bogs and absent from the Alps. However, the researchers suggest that in earlier cold phases – some 22,000 years ago – the swamp porst and the alpine rose did share a habitat in perialpine lowland habitats north of the Alps. It is very likely that after the last cold period and the melting of the glaciers, some populations of the species shifted their host preference from the swamp porst to the alpine rose. The separation of the distribution areas of the two plants caused by subsequent warm phases inevitably led to the separation of the moth populations.

Extinction risk

Characteristic cocoon with final instar larva and pupa of the alpine rose leaf-miner moth on *Rhododendron ferrugineum* in Ardez, Graubünden, Switzerland. Photos by Jürg Schmid

The Alpine Rose Leaf-miner Moth is so far only known from the Lower Engadine. It lives in a steep, north-exposed, spruce-larch-pine forest at about 1,800 m above sea level. The high snow coverage in winter and the largely shady conditions in summer mean that alpine roses don’t get to bloom there. The scientists suspect that the moth species can still be discovered in places with similar conditions in the northern Alps, such as in neighboring Tyrol and Vorarlberg. Since the moth is likely nocturnal and flies late in the year, probably hibernating in the adult stage, the search for the caterpillars and pupae is more promising. However, the special microclimate of the Swiss location does not suggest that this species, which has so far been overlooked despite 250 years of research, is widespread. On the contrary, there are legitimate concerns that it could be one of the first victims of climate change.

Research article:

Huemer P, Schmid J (2021) Relict populations of Lyonetia ledi Wocke, 1859 (Lepidoptera, Lyonetiidae) from the Alps indicate postglacial host-plant shift to the famous Alpenrose (Rhododendron ferrugineum L.). Alpine Entomology 5: 101-106. https://doi.org/10.3897/alpento.5.76930